Yang Rong, Zheng Zhimin, Chen Qing, Yang Lan, Huang Huan, Miki Daisuke, Wu Wenwu, Zeng Liang, Liu Jun, Zhou Jin-Xing, Ogas Joe, Zhu Jian-Kang, He Xin-Jian, Zhang Heng
Shanghai Center for Plant Stress Biology, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, Shanghai, 210602, China.
National Institute of Biological Sciences, Beijing, 102206, China.
Genome Biol. 2017 May 31;18(1):103. doi: 10.1186/s13059-017-1226-y.
The chromodomain helicase DNA-binding family of ATP-dependent chromatin remodeling factors play essential roles during eukaryote growth and development. They are recruited by specific transcription factors and regulate the expression of developmentally important genes. Here, we describe an unexpected role in non-coding RNA-directed DNA methylation in Arabidopsis thaliana.
Through forward genetic screens we identified PKL, a gene required for developmental regulation in plants, as a factor promoting transcriptional silencing at the transgenic RD29A promoter. Mutation of PKL results in DNA methylation changes at more than half of the loci that are targeted by RNA-directed DNA methylation (RdDM). A small number of transposable elements and genes had reduced DNA methylation correlated with derepression in the pkl mutant, though for the majority, decreases in DNA methylation are not sufficient to cause release of silencing. The changes in DNA methylation in the pkl mutant are positively correlated with changes in 24-nt siRNA levels. In addition, PKL is required for the accumulation of Pol V-dependent transcripts and for the positioning of Pol V-stabilized nucleosomes at several tested loci, indicating that RNA polymerase V-related functions are impaired in the pkl mutant.
PKL is required for transcriptional silencing and has significant effects on RdDM in plants. The changes in DNA methylation in the pkl mutant are correlated with changes in the non-coding RNAs produced by Pol IV and Pol V. We propose that at RdDM target regions, PKL may be required to create a chromatin environment that influences non-coding RNA production, DNA methylation, and transcriptional silencing.
ATP依赖的染色质重塑因子的色域解旋酶DNA结合家族在真核生物生长和发育过程中发挥着重要作用。它们被特定的转录因子招募，并调节发育重要基因的表达。在这里，我们描述了拟南芥中一个在非编码RNA介导的DNA甲基化中的意外作用。
通过正向遗传学筛选，我们鉴定出PKL，一个植物发育调控所需的基因，是促进转基因RD29A启动子转录沉默的一个因子。PKL的突变导致超过一半的RNA介导的DNA甲基化（RdDM）靶向位点的DNA甲基化发生变化。少数转座元件和基因的DNA甲基化减少，与pkl突变体中的去抑制相关，尽管对于大多数而言，DNA甲基化的减少不足以导致沉默的释放。pkl突变体中DNA甲基化的变化与24-nt siRNA水平的变化呈正相关。此外，PKL是Pol V依赖转录本积累以及在几个测试位点定位Pol V稳定核小体所必需的，这表明pkl突变体中RNA聚合酶V相关功能受损。
PKL是转录沉默所必需的，并且对植物中的RdDM有显著影响。pkl突变体中DNA甲基化的变化与Pol IV和Pol V产生的非编码RNA变化相关。我们提出，在RdDM靶区域，可能需要PKL来创建一个影响非编码RNA产生、DNA甲基化和转录沉默的染色质环境。
